From d038d6822ae971f9c91243d8141f91c23b1dec52 Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Thu, 14 Dec 2023 14:09:43 -0800
Subject: [PATCH] Update H3N2 titer references

---
 config/references_for_titer_plots_h3n2.txt    | 50 +++++++++----------
 config/subclades_for_titer_plots_h3n2.txt     |  2 +-
 ...lot_antigenic_distances_between_strains.py |  6 ++-
 3 files changed, 30 insertions(+), 28 deletions(-)

diff --git a/config/references_for_titer_plots_h3n2.txt b/config/references_for_titer_plots_h3n2.txt
index 0b1b2e5b..8b4315fc 100644
--- a/config/references_for_titer_plots_h3n2.txt
+++ b/config/references_for_titer_plots_h3n2.txt
@@ -1,26 +1,24 @@
-A/Darwin/6/2021
-A/Michigan/60/2022
-A/SouthAustralia/1/2023
-A/Poland/97/2022
-A/Norway/24873/2021
-A/Hyogo/3001/2022
-A/Massachusetts/18/2022
-A/Shimane/1/2022
-A/Thailand/8/2022
-A/Perth/186/2022
-A/Florida/57/2022
-A/SouthAfrica/R08120/2022
-A/Thuringen/10/2022
-A/Darwin/2475/2022
-A/Victoria/164/2023
-A/Montana/8/2023
-A/SouthAustralia/389/2022
-A/SouthAustralia/380/2022
-A/Kanagawa/ZC2201/2022
-A/Darwin/9/2021-egg
-A/Darwin/6/2021-egg
-A/Victoria/39/2022-egg
-A/Canberra/1/2022-egg
-A/Norway/24873/2021-egg
-A/Thailand/8/2022-egg
-A/Albania/289813/2022-egg
+A/Massachusetts/18/2022 # H
+A/Hyogo/3001/2022 # H
+A/Shimane/1/2022 # H
+A/Thailand/8/2022 # H for HI
+A/NewYork/66/2022 # H:122D
+A/SouthAustralia/48/2023 # H:122D
+A/Albania/289813/2022 # H:91N,122D for HI
+A/Darwin/6/2021 # G.1:53G
+A/Michigan/60/2022 # G.1.1.2
+A/SouthAustralia/1/2023 # G.1.1.2 for HI
+A/Poland/97/2022 # G.1.2:4S,25V,145N for HI
+A/Florida/57/2022 # G.2
+A/Montana/8/2023 # G.2.1
+A/SouthAustralia/389/2022 # G.2.1 for HI
+A/SouthAustralia/380/2022 # G.2.2 for HI
+A/Kanagawa/ZC2201/2022 # G.2.2
+A/California/122/2022-egg # H
+A/Thailand/8/2022-egg # H
+A/California/122/2022-egg # H for HI
+A/Brandenburg/15/2022-egg # H for HI
+A/Albania/289813/2022-egg # H:91N,122D for HI
+A/Darwin/9/2021-egg # G.1
+A/SouthAustralia/389/2022-egg # G.2.1
+A/Darwin/6/2021-egg # G.1:53G
diff --git a/config/subclades_for_titer_plots_h3n2.txt b/config/subclades_for_titer_plots_h3n2.txt
index f1c3aa44..065501c4 100644
--- a/config/subclades_for_titer_plots_h3n2.txt
+++ b/config/subclades_for_titer_plots_h3n2.txt
@@ -1,6 +1,6 @@
+H
 G.1.1.2
 G.1.3.1
-H
 G.1.3.2
 G.2
 G.2.1
diff --git a/scripts/plot_antigenic_distances_between_strains.py b/scripts/plot_antigenic_distances_between_strains.py
index 7cc8a63e..135d0cc6 100644
--- a/scripts/plot_antigenic_distances_between_strains.py
+++ b/scripts/plot_antigenic_distances_between_strains.py
@@ -237,7 +237,11 @@
     left = xticks[0]
     right = xticks[-1]
     width = right - left
-    height = yticks[1] - yticks[0]
+
+    if len(yticks) > 1:
+        height = yticks[1] - yticks[0]
+    else:
+        height = 1
 
     # create bars at yticks that are the length of our greatest xtick and have a height equal to our tick spacing
     ax.barh(